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:root {
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    --select-text-bg-color:#4a89dc;

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html {
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html,
body {
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#write {
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html,
body,
button,
input,
select,
textarea,
div.code-tooltip-content {
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div.code-tooltip,
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button,
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select,
textarea {
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hr {
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h2 {
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sup.md-footnote {
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ul,
dd,
ol,
hr,
address,
pre,
table,
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li > blockquote {
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*.in-text-selection,
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ol {
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ol ol,
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ol ul {
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th,
dt,
strong {
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i,
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dfn,
cite {
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blockquote {
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code,
kbd,
tt,
var {
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kbd {
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code,
kbd,
tt,
var {
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table {
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th,
td {
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a {
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hr {
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h1 {
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}

a {
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a:hover {
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.md-inline-math script {
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b,
th,
dt,
strong {
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mark {
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blockquote {
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table a {
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th,
td {
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}

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#write pre.md-meta-block {
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}

.btn,
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}

.ty-table-edit {
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#write>h4:before,
#write>h5:before,
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h1.md-focus .md-attr,
h2.md-focus .md-attr,
h3.md-focus .md-attr,
h4.md-focus .md-attr,
h5.md-focus .md-attr,
h6.md-focus .md-attr,
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}

.md-comment {
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.modal-backdrop {
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.modal-content .btn-primary {
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.md-table-resize-popover {
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.form-inline .input-group .input-group-addon {
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/** UI for electron */

.context-menu,
#spell-check-panel,
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footer {
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@media (max-width: 1000px) {
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}

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.megamenu-content,
.megamenu-opened header {
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.active-tab-files #info-panel-tab-file,
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<div  id='write'  class = 'is-mac'><h1><a name='header-n0' class='md-header-anchor '></a>Synteny analysis using SynChro</h1><p><strong><em>This tutorial takes EMBL/Genbank genome files or genome FASTAs and GFF annotations, extracts protein FASTA records from FASTAs and GFFs, and runs the genomes through SynChro.</em></strong> <em>Here we use this protocol to get genome files from</em> Gallus gallus <em>and</em> Anolis carolinensis, <em>and genome FASTA and GFF annotation from</em> Gopherus agassizii. <em>We pull protein FASTA records from</em> Gopherus agassizii <em>and isolate proteins from the top 26 scaffolds with the most genes. We input these files into the CHROnicle directory and run SynChro to create macrosynteny figures.</em></p><p>&nbsp;</p><h3><a name='header-n4' class='md-header-anchor '></a>Step 1: Clone in GitHub repository at <a href='https://github.com/mmoral31/GopAga2.0-Genome.git' target='_blank' class='url'>https://github.com/mmoral31/GopAga2.0-Genome.git</a></h3><p><em>The scripts will run straight out of the box (note—these were only tested on unix and linux platforms)</em></p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; <span class="cm-builtin">git</span> clone https://github.com/mmoral31/GopAga2.0-Genome.git</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 26px;"></div><div class="CodeMirror-gutters" style="display: none; height: 26px;"></div></div></div></pre><p>&nbsp;</p><h3><a name='header-n8' class='md-header-anchor '></a>Step 2: Gather your genome and annotation files</h3><p><strong>If your species&#39; genome files are available on EMBL or Genbank (.dat) they can be downloaded from ftp.ensembl.org for easy use. </strong></p><p>EMBL or Genbank genome files on Ensembl are easily converted for use in SynChro. However, if your species of interest does not have these files, in <strong>steps 3–5 below</strong> you can use genome FASTA and GFF3 annotation files for use in SynChro, which requires specific formatting.</p><p>&nbsp;</p><h3><a name='header-n12' class='md-header-anchor '></a>Step 3: Use gff2fasta.pl to modify FASTA records with info from annotation file.</h3><blockquote><p>Requires BioPerl</p></blockquote><p>to use genome FASTAs and GFF annotations in SynChro, protein FASTA records must be extracted from both files and supplemented with data on gene position and scaffold. this modified gff2fasta.pl script will perform this task.</p><p>gff2fasta.pl takes three parameters in this order:</p><ul><li>genome FASTA for species of interest (e.g., Cmyd_genome.fa)</li><li>GFF annotation for species of interest (e.g., Cmyd_annotation.gff)</li><li>shortened species name for use in the prefix of output files (e.g., Cmyd)</li></ul><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; perl gff2fasta.pl Cmyd_genome.fa Cmyd_annotation.gff Cmyd</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 26px;"></div><div class="CodeMirror-gutters" style="display: none; height: 26px;"></div></div></div></pre><p>Note, we modified this script from <a href='https://github.com/ISUgenomics/common_scripts/blob/master/gff2fasta.pl' target='_blank' class='url'>https://github.com/ISUgenomics/common_scripts/blob/master/gff2fasta.pl</a>. Our modifications in this version are the addition of gene start, gene end, strand, and scaffold data for each gene to its respective protein fasta ID.</p><p>output file for further curation will be named {shortened species name}.pep.fasta (e.g., Cmyd.pep.fasta)</p><p><em>e.g., output headers:</em></p><blockquote><blockquote><p><strong>gopAga2_0-00023227-RA 113463 126175 + ScCC6lQ_11006_HRSCAF_31022</strong>
MAGESHVIRKMKVSSFHHGPVMSSSLPGYIMFFIILSIHKGDSAQFKVIGPDHPVMATAG
EDIVLPCHLSPRVSTENMEVRWYRSQFYSLVHLYRDGDNQNERQMPEYQGRTEFLRDDIA</p></blockquote></blockquote><h3><a name='header-n31' class='md-header-anchor '></a>Step 4: [optional] Reduce SynChro memory footprint</h3><p><strong>use pull_id_match.py to isolate proteins from a user-specified number of scaffolds.</strong></p><blockquote><p>Requires Biopython</p></blockquote><p>Preliminary analyses using SynChro with protein FASTAs showed that genomes with genes spread across too many scaffolds will quickly reach memory limitations. To combat this, we ran SynChro on a reduced number of genes pulled from the 26 most gene-dense scaffolds. This provided sufficient genome coverage to assess synteny without hitting memory issues.</p><p>first, parse the protein FASTA of the species of interest to determine scaffolds with the most genes.</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-builtin">grep</span> <span class="cm-string">'&gt;'</span> Cmyd_proteins.fa | <span class="cm-builtin">cut</span> <span class="cm-attribute">-d</span> <span class="cm-string">" "</span> <span class="cm-attribute">-f5</span> | <span class="cm-builtin">sort</span> | uniq <span class="cm-attribute">-c</span> | <span class="cm-builtin">sort</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 26px;"></div><div class="CodeMirror-gutters" style="display: none; height: 26px;"></div></div></div></pre><p>example output (first column is # of genes):</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash" style="page-break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">364</span> ScCC6lQ_38465_HRSCAF_64658</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">376</span> ScCC6lQ_161303_HRSCAF_192837</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">395</span> ScCC6lQ_161354_HRSCAF_192888</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">401</span> ScCC6lQ_3500_HRSCAF_17357</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">406</span> ScCC6lQ_97_HRSCAF_1492</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">415</span> ScCC6lQ_28138_HRSCAF_52803</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">420</span> ScCC6lQ_3789_HRSCAF_18069</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">429</span> ScCC6lQ_161370_HRSCAF_192904</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">446</span> ScCC6lQ_14958_HRSCAF_36502</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">450</span> ScCC6lQ_161315_HRSCAF_192849</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">454</span> ScCC6lQ_3764_HRSCAF_18001</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">455</span> ScCC6lQ_40749_HRSCAF_67263</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">503</span> ScCC6lQ_161394_HRSCAF_192928</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">508</span> ScCC6lQ_24292_HRSCAF_48220</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">528</span> ScCC6lQ_140_HRSCAF_2235</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">580</span> ScCC6lQ_1923_HRSCAF_13295</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">715</span> ScCC6lQ_16796_HRSCAF_38896</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">718</span> ScCC6lQ_161421_HRSCAF_192955</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-number">861</span> ScCC6lQ_161298_HRSCAF_192832</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 494px;"></div><div class="CodeMirror-gutters" style="display: none; height: 494px;"></div></div></div></pre><p>then, create a text file with the names of desired scaffolds; one scaffold name per line.</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">ScCC6lQ_14958_HRSCAF_36502</span></pre></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">ScCC6lQ_161315_HRSCAF_192849</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">ScCC6lQ_3764_HRSCAF_18001</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">ScCC6lQ_40749_HRSCAF_67263</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">ScCC6lQ_161394_HRSCAF_192928</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">.</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">.</span></pre><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">.</span></pre></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 208px;"></div><div class="CodeMirror-gutters" style="display: none; height: 208px;"></div></div></div></pre><p>run <strong><em>pull_id_match.py</em></strong> to isolate proteins from desired scaffolds.</p><p><em>pull_id_match.py</em> takes three parameters in this order:</p><ul><li>name of protein FASTA file to pull from (e.g., Cmyd_proteins.fa)</li><li>name of text file with list of desired scaffolds (e.g., Cmyd_scaffolds.txt)</li><li>name of output FASTA file (e.g., Cmyd_protreduct.fa)</li></ul><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; python pull_id_match.py Cmyd_proteins.fa Cmyd_scaffolds.txt Cmyd_protreduct.fasta</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 26px;"></div><div class="CodeMirror-gutters" style="display: none; height: 26px;"></div></div></div></pre><p>&nbsp;</p><h3><a name='header-n53' class='md-header-anchor '></a>Step 5: Convert files to SynChro format </h3><p><strong>Using ConvertGbk.py, ConvertEMBL.py, or ConvertFasta.py for Genbank, EMBL, and protein FASTA files respectively, convert input files to SynChro format</strong></p><blockquote><p>Requires CHROnicle </p></blockquote><p>genome files and protein FASTAs must now be converted to SynChro format for analyses. <strong>from this point forward, all scripts are run from inside the CHROnicle folder</strong> (download here: <a href='http://www.lcqb.upmc.fr/CHROnicle/SynChro.html' target='_blank' class='url'>http://www.lcqb.upmc.fr/CHROnicle/SynChro.html</a>](<a href='http://www.lcqb.upmc.fr/CHROnicle/SynChro.html' target='_blank' class='url'>http://www.lcqb.upmc.fr/CHROnicle/SynChro.html</a>). </p><p>create a directory for the current synteny analysis (e.g. Reptiles). Inside this directory, create a directory &quot;00rawGenom&quot;. In this directory, create a directory for each species in the analysis (e.g., CheloniaMydas, GopherusAgassizii, etc.). In each of these directories, place the respective genome files or protein FASTAs. </p><blockquote><p><em>e.g., /SynChro/00rawGenom/CheloniaMydas</em></p></blockquote><p>from the top level of the CHROnicle directory, cd into the &quot;Programs/0Convert2InputF&quot; directory. From here, run one of three scripts (<em>ConvertGbk.py</em>, <em>ConvertEMBL.py</em>, or <em>ConvertFasta.py</em>) for each species (see below).</p><p>&nbsp;</p><p><strong>all scripts require at least three parameters in this order:</strong></p><ul><li>name of the directory for the current macrosynteny analysis (e.g. Reptiles)</li><li>name of the directory for the target species (e.g. CheloniaMydas)</li><li>shortened species name for output files (e.g. CMYD)</li></ul><p>if the target species has <strong><em>Genbank genome files</em></strong>, run ConvertGbk.py with no additional parameters.</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; ./ConvertGbk.py Reptiles CheloniaMydas CMYD</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 26px;"></div><div class="CodeMirror-gutters" style="display: none; height: 26px;"></div></div></div></pre><p>if the target species has <strong><em>EMBL genome files</em></strong>, run ConvertEMBL.py with no additional parameters.</p><pre spellcheck="false" class="md-fences md-end-block ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 0px; left: 4px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 0px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: 0px; width: 0px;"></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">&gt; ./ConvertEMBL.py Reptiles CheloniaMydas CMYD</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom-width: 0px; border-bottom-style: solid; border-bottom-color: transparent; top: 26px;"></div><div class="CodeMirror-gutters" style="display: none; height: 26px;"></div></div></div></pre><p>if the target species has <strong><em>a protein FASTA</em></strong>, run ConvertFasta.py with additional parameters specifying the columns of each protein FASTA record ID that contain information on gene name, scaffold, start, end, and strand. The last parameter specifies whether the protein FASTA is sorted or not. <strong>the example parameterization is sufficient for output from <em>gff2fasta.pl</em></strong> (step 3 above).</p><p><em>note: ConvertFasta.py will only work if protein FASTA has the suffix &quot;.fasta&quot; and will otherwise throw an InputF error</em></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n77" mdtype="fences">&gt; ./ConvertFasta.py Reptiles CheloniaMydas CMYD 1 5 2 3 4 0
</pre><p>&nbsp;</p><h3><a name='header-n79' class='md-header-anchor '></a>Step 6: Run SynChro.py </h3><p>now, SynChro.py can be run to perform synteny between your genomes of interest.</p><p>from the top level of the CHROnicle directory, move into the &quot;Programs/1SynChro&quot; directory. from here, run SynChro.py once.</p><p>SynChro.py takes three parameters in this order:</p><ul><li>name of the directory for the current macrosynteny analysis (e.g. Reptiles)</li><li>parameter set to 0 if all species in the directory are to be analyzed or 1 if only a select few are to be analyzed</li><li>delta value which specifies how many orthologous genes need to be syntenic in both genomes to be considered a synteny block (for more information, visit: <a href='http://www.lcqb.upmc.fr/CHROnicle/SynChro.html'>http://www.lcqb.upmc.fr/CHROnicle/SynChro.html</a>)</li></ul><p><em>note: delta=2 is the defualt, here we are running a slightly more conservative delta=4, but this setting did not have a qualitative effect on our results</em></p><pre spellcheck="false" class="md-fences mock-cm md-end-block" lang="bash" contenteditable="false" cid="n91" mdtype="fences">&gt; ./SynChro.py Reptiles 0 4
</pre><p>The output will be a series of svg files showing different aspects of synteny that can be modified in Illustrator.</p></div>
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